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This document specifies the general requirements for the in vitro amplification of nucleic acid sequences (DNA or RNA). This includes polymerase chain reaction (PCR)-based methods like quantitative PCR, qualitative PCR, reverse transcription-PCR and digital PCR. The minimum requirements laid down in this document are intended to ensure that comparable and reproducible results are obtained in different organizations. It covers quality assurance aspects to be considered when working with PCR-based methods in a laboratory as well as validation and verification. In addition to laboratory PCR-based methods, this document is also applicable to on-site PCR-based methods. This document is applicable to PCR-based methods used for the analysis of microorganisms and viruses in different water matrices, including but not limited to: This document is applicable to the detection and quantification of nucleic acids (DNA or RNA) of microorganisms by PCR-based methods in water such as bacteria, yeasts, fungi but also parasites such as Cryptosporidium, Giardia, amoebas and multicellular organisms. In addition, this document is applicable to the detection and quantification of nucleic acids from viruses in water by PCR-based methods.